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yh202109 committed Jul 21, 2024
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4 changes: 2 additions & 2 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
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2 changes: 1 addition & 1 deletion _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
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<?xml version="1.0" ?>
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<sources>
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8 changes: 4 additions & 4 deletions _sources/statlab_kappa2.rst.txt
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Expand Up @@ -296,7 +296,6 @@ The first element of :eq:`eq_kappa2_vn2` can be calculated as [2]_ :sup:`(Eq. 12
E\left(\sum_{j} N_{ij}^4\right)
= R + 7R(R-1)\sum_j p_j^2 + 6R(R-1)(R-2)\sum_j p_j^3 + R(R-1)(R-2)(R-3)\sum_j p_j^4
The third element of :eq:`eq_kappa2_vn2` can be calculated as [2]_ :sup:`(Eq. 14)`

.. math::
Expand All @@ -306,13 +305,14 @@ The third element of :eq:`eq_kappa2_vn2` can be calculated as [2]_ :sup:`(Eq. 14
=& R^2\left(1 + (R-1)\sum_{j} p_j^2 \right)^2 \\
=& R^2 + R^2(R-1)\left(2\sum_{j} p_j^2 + (R-1)(\sum_j p_j^2)^2\right)
The second element of :eq:`eq_kappa2_vn2` can be calculated using
The second element of :eq:`eq_kappa2_vn2` can be calculated, using
:math:`E\left( N_{ij}^2 N_{ik}^2 \right) = R(R-1)p_j(p_k+(R-2)p_k^2) + R(R-1)(R-2)p_j^2(p_k+(R-3)p_k^2)`, as

.. math::
:label: eq_kappa2_vn5
E\left( N_{ij}^2 N_{ik}^2 \right)
= R(R-1)p_j(p_k+(R-2)p_k^2) + R(R-1)(R-2)p_j^2(p_k+(R-3)p_k^2)
E\left( \sum_j\sum_{k \neq j} N_{ij}^2 N_{ik}^2 \right)
=& R(R-1) + R(R-1)(2R-5)(\sum_j p_j^2) - 2R(R-1)(R-2)(\sum_j p_j^3) - R(R-1)(R-2)(R-3) \sum_j p_j^4 + R(R-1)(R-2)(R-3) (\sum_{j} p_j^2)^2
Combining :eq:`eq_kappa2_vn3`, :eq:`eq_kappa2_vn4`, and :eq:`eq_kappa2_vn5`,
:eq:`eq_kappa2_vn2` can be calculated as [2]_ :sup:`(Eq. 15)`
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2 changes: 1 addition & 1 deletion _static/reports/coverage/coverage.xml
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<?xml version="1.0" ?>
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<sources>
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2 changes: 1 addition & 1 deletion _static/reports/junit/junit.xml
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<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="38" time="8.802" timestamp="2024-07-21T18:53:26.025859+00:00" hostname="fv-az1055-998"><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_invalid_input" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_missing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_with_difference" time="0.005" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_without_difference" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_existing_column" time="0.010" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_group" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_same_group_and_column" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_include" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_outfmt" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_load_list" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_show_ctoc_tree" time="0.197" /><testcase classname="tests.test_health_emt.TestEmt" name="test_expected_file_lists" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_files" time="0.005" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlgt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_llt" time="0.007" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc_primary_only" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_soc" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_list_files" time="0.025" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_dataframe" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_json" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_list" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_string" time="0.000" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree" time="0.013" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree2" time="0.008" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_dataframe" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_list" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_plot_y_list" time="0.017" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_bootstrap_cohen_ci" time="0.231" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_cohen" time="0.068" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.065" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.765" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.864" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.834" /></testsuite></testsuites>
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4 changes: 2 additions & 2 deletions _static/reports/junit/report.html
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10 changes: 2 additions & 8 deletions example_cdtg.html
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Expand Up @@ -133,13 +133,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 15.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
warnings.warn(msg, UserWarning)
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 10.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
warnings.warn(msg, UserWarning)
</pre></div>
</div>
<img alt="_images/933969f373f160b503820ede7fca91e75ac216d5454ffd427d75f27fef3b9a90.png" src="_images/933969f373f160b503820ede7fca91e75ac216d5454ffd427d75f27fef3b9a90.png" />
<img alt="_images/1ff8a44423a7ab6e1f637ef0f22e7eb5d21cf1f16d9733c46fa776aba8941598.png" src="_images/1ff8a44423a7ab6e1f637ef0f22e7eb5d21cf1f16d9733c46fa776aba8941598.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -151,7 +145,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/edbcb05be23c6de576d319f47189a8a15a4645ca09a373ee63d85bfe47ce2cb0.png" src="_images/edbcb05be23c6de576d319f47189a8a15a4645ca09a373ee63d85bfe47ce2cb0.png" />
<img alt="_images/b9c3389ce39ca8d59b3ccd9a0450634aeb3dcc7189c20724cec73c62993a421c.png" src="_images/b9c3389ce39ca8d59b3ccd9a0450634aeb3dcc7189c20724cec73c62993a421c.png" />
</div>
</div>
</section>
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72 changes: 36 additions & 36 deletions example_clinical.html
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Expand Up @@ -131,8 +131,8 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit meal calorie
0 STD1 TRT1 SUBJ01 VISIT1 1 1208
1 STD1 TRT1 SUBJ01 VISIT1 2 1398
0 STD1 TRT1 SUBJ01 VISIT1 1 1702
1 STD1 TRT1 SUBJ01 VISIT1 2 1523
</pre></div>
</div>
</div>
Expand All @@ -149,12 +149,12 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit N(0&lt;=X&lt;500) N(500&lt;=X&lt;1000) \
0 STD1 TRT1 SUBJ01 VISIT1 1 2
1 STD1 TRT1 SUBJ02 VISIT1 0 1
0 STD1 TRT1 SUBJ01 VISIT1 0 0
1 STD1 TRT1 SUBJ01 VISIT2 0 2

N(1000&lt;=V&lt;=2000) N(all)
0 2 5
1 1 2
0 2 2
1 3 5
</pre></div>
</div>
</div>
Expand All @@ -169,22 +169,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit N(0&lt;=X&lt;3) N(3&lt;=X&lt;5) N(5&lt;=V&lt;=7) N(all)
0 STD1 TRT1 VISIT1 5 9 6 20
1 STD1 TRT1 VISIT2 4 9 4 17
2 STD1 TRT1 VISIT3 1 8 4 13
0 STD1 TRT1 VISIT1 4 9 7 20
1 STD1 TRT1 VISIT2 1 13 6 20
2 STD1 TRT1 VISIT3 3 6 6 15
3 STD1 TRT1 VISIT4 3 3 0 6
4 STD1 TRT2 VISIT1 3 15 2 20
5 STD1 TRT2 VISIT2 1 10 2 13
6 STD1 TRT2 VISIT3 3 4 2 9
7 STD1 TRT2 VISIT4 1 2 1 4
8 STD2 TRT1 VISIT1 7 9 4 20
9 STD2 TRT1 VISIT2 5 6 5 16
10 STD2 TRT1 VISIT3 4 7 3 14
11 STD2 TRT1 VISIT4 2 0 0 2
12 STD2 TRT2 VISIT1 4 8 8 20
13 STD2 TRT2 VISIT2 4 11 3 18
14 STD2 TRT2 VISIT3 4 6 2 12
15 STD2 TRT2 VISIT4 3 3 2 8
4 STD1 TRT2 VISIT1 7 7 6 20
5 STD1 TRT2 VISIT2 3 9 5 17
6 STD1 TRT2 VISIT3 1 5 5 11
7 STD1 TRT2 VISIT4 1 1 1 3
8 STD2 TRT1 VISIT1 3 11 6 20
9 STD2 TRT1 VISIT2 3 6 7 16
10 STD2 TRT1 VISIT3 4 8 1 13
11 STD2 TRT1 VISIT4 0 3 3 6
12 STD2 TRT2 VISIT1 6 10 4 20
13 STD2 TRT2 VISIT2 5 7 2 14
14 STD2 TRT2 VISIT3 2 4 5 11
15 STD2 TRT2 VISIT4 2 2 2 6
</pre></div>
</div>
</div>
Expand All @@ -198,22 +198,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit Sum(0&lt;=X&lt;3) Sum(3&lt;=X&lt;5) Sum(5&lt;=V&lt;=7) Sum(all)
0 STD1 TRT1 VISIT1 10 33 30 73
1 STD1 TRT1 VISIT2 8 31 20 59
2 STD1 TRT1 VISIT3 2 27 20 49
0 STD1 TRT1 VISIT1 8 33 35 76
1 STD1 TRT1 VISIT2 2 47 30 79
2 STD1 TRT1 VISIT3 6 21 30 57
3 STD1 TRT1 VISIT4 6 10 0 16
4 STD1 TRT2 VISIT1 6 53 10 69
5 STD1 TRT2 VISIT2 2 32 10 44
6 STD1 TRT2 VISIT3 6 14 10 30
7 STD1 TRT2 VISIT4 2 8 5 15
8 STD2 TRT1 VISIT1 14 29 20 63
9 STD2 TRT1 VISIT2 10 20 25 55
10 STD2 TRT1 VISIT3 8 24 15 47
11 STD2 TRT1 VISIT4 4 0 0 4
12 STD2 TRT2 VISIT1 8 29 40 77
13 STD2 TRT2 VISIT2 8 39 15 62
14 STD2 TRT2 VISIT3 8 20 10 38
15 STD2 TRT2 VISIT4 6 11 10 27
4 STD1 TRT2 VISIT1 14 24 30 68
5 STD1 TRT2 VISIT2 6 32 25 63
6 STD1 TRT2 VISIT3 2 17 25 44
7 STD1 TRT2 VISIT4 2 3 5 10
8 STD2 TRT1 VISIT1 6 41 30 77
9 STD2 TRT1 VISIT2 6 20 35 61
10 STD2 TRT1 VISIT3 8 27 5 40
11 STD2 TRT1 VISIT4 0 12 15 27
12 STD2 TRT2 VISIT1 12 35 20 67
13 STD2 TRT2 VISIT2 10 25 10 45
14 STD2 TRT2 VISIT3 4 15 25 44
15 STD2 TRT2 VISIT4 4 7 10 21
</pre></div>
</div>
</div>
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